Technical Overview,

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This script displays the proteins in a GPM result file divided into categories defined by Normal_Clinical_Tissue_Alliance from selected BRENDA identifiers.

The required arguments are path, proex and ltype. path is the file system path to the GPM result file. proex is used to create links to other scripts on GPMDB. ltype controls the appearance of display elements on the page. Optional parameters are npep, taxa, k, all and sumI all of which are used in generating links to additional GPM resources, with the exception of k, which controls the sorting of the results.

Display Elements

  • a list of links to further GPMDB and external resources.
  • the table of results:
    • BTO ID: the identifier for a specific tissue type.
    • Tissue: the name of the tissue.
    • log(I): the base-10 logarithm of the raw intensities observed for the proteins within a single pathway.
    • log(p)+: the base-10 logarithm of the chances that the collection of proteins assigned to this pathway is random.
    • protein description: a compound field:
      • a bar graph depicting the relative distribution of the proteins in the GPM result file per BTO category, and notation describing if the distribution is enriched, normal or depleted.
      • X/Y of Z: X proteins in the model correspond to that category; Y proteins would be expected if the proteins were evenly distributed; and Z is the total number of protein accessions with that BRENDA annotation.
      • a list of the proteins from the GPM result file which fall into this BTO category, including links to further GPM and external resources regarding this protein.
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